Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition

Huang T, Bruderer R, Muntel J, Xuan Y, Vitek O, and Reiter L. Molecular & Cellular Proteomics.

In this publication, we report a novel statistical procedure that takes advantage of the two independent quantitative spaces available in DIA data, i.e., MS1 and MS2, for the detection of differentially abundant proteins. The use of these two levels improves precision and reduces the effect of the interferences. This new approach was applied to six sets of controlled mixtures, showing a consistent improvement in the ability to find differential changes at the protein level.

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